Re: [ccp4bb] Topology diagram

[Andy Purkiss]

Dear Lionel and Xavier,

Unfortunately TOPDRAW doesn't interpret a pdb file, it just allows you to draw 
your own topology diagram.

PDBSUM (available from https://www.ebi.ac.uk/thornton-srv/software/PDBsum1/) 
has a topology diagram as part of the output.

You can also access a database of released structures here: 
https://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ and there is a link to the 
Generate webpage there allows you to  securely upload a pdb file if you don't 
wish to install the software yourself.

Hope this helps,

Andy Purkiss


From: CCP4 bulletin board  on behalf of Xavier 
Brazzolotto 
Sent: 30 May 2024 16:39
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Topology diagram


External Sender: Use caution.

My Google search led directly to

<https://www.ccp4.ac.uk/html/topdraw.html>
TOPDRAW (CCP4: Supported Program) — CCP4 
documentation<https://www.ccp4.ac.uk/html/topdraw.html>
ccp4.ac.uk<https://www.ccp4.ac.uk/html/topdraw.html>
[favicon.ico]<https://www.ccp4.ac.uk/html/topdraw.html>

HTH

Le 30 mai 2024 à 17:32, Lionel  a écrit :

Dear community,

A biochemist asks me if I knew a webserver/tool to draw topology diagram of 
protein from a deposited pdb or part of it, ideally allowing edition (label, 
colour, etc...).

For a better understanding, the topology diagram’s representation is as the 
picture attached, which I believe is a “key notation” topology diagram.

It’s possible to get such diagram from PDBsum but they are fixed (pdf, ps) and 
I would say (without offence) a bit ugly.

After an extensive Google/Ccp4DB/ChatGPT search, for my surprise, I found 
nothing helpful.
It seems that “old” tools like pro-origami are gone/unavailable.

I would greatly appreciate any advice on possible website or more specialized 
program (even if I would do the “webserver” task myself).

Best,
Lionel




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Re: [ccp4bb] a dinosaur asks ... PDB format query

[Andy Purkiss]

For those wanting a text editor solution, there is the purpose built pdb-mode 
plugin for (x)emacs which works under most operating systems.

The download location has moved around a bit, but a current version is 
available from
https://github.com/mmagnus/emacs-pdb-mode/

with more details at
https://bondxray.org/software/pdb-mode/

Hope this helps,

Andy Purkiss


From: CCP4 bulletin board  on behalf of Hughes, Jonathan 

Sent: 15 May 2024 13:11
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query


External Sender: Use caution.


hello CCP4 people,
rather off-topic: is there a purpose-written windows editor for PDF files? with 
interleaved anisotropy lines, missing column delimiters etc., simply extracting 
the B-factors for Ca atoms is hard work using a standard character editor. 
would anyone think of working with DNA without proper tools?
best
jon

--
Prof. Dr. Jon Hughes
Department of Physics
Free University of Berlin
&
Institute for Plant Physiology
Justus Liebig University
Giessen
Germany




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Re: [ccp4bb] replacement for Scientific Linux

[Andy Purkiss]

Hi Harry,

We've been migrating to Rocky Linux as it is built on RHEL in a similar way to 
Scientific Linux. Most things compiled on Centos 7 (our default for a while) 
work in Rocky Linux version 9. For compilers etc., I use the Software 
Collections / devtoolsets to run later versions than the default OS.

Hope this helps,

Andy


From: CCP4 bulletin board  on behalf of Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Sent: 26 April 2024 16:46
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] replacement for Scientific Linux


External Sender: Use caution.


Hi folks

For many years I’ve been using Scientific Linux as my OS of choice (when not 
using my Mac) - but it’s been discontinued. SL was based on RHEL, and had 
useful things like a less-buggy Fortran/C/C++ compiler than that released by RH.

What do people here recommend as a replacement?

Harry


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Re: [ccp4bb] add ligand with AceDRG

[Andy Purkiss]

Hi Stefanie,

In CCP4Cloud, the equivalent task will generate the files using a 'free', 
unused code, if nothing is entered in the relevant box. However, not sure if 
CCP4I2's task will do the same, but worth trying.

Hope this helps,

Andy


From: CCP4 bulletin board  on behalf of FREITAG-POHL, 
STEFANIE 
Sent: 25 April 2024 13:01
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] add ligand with AceDRG


External Sender: Use caution.

Hi all,

I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:

I put in a smilesstring and the ligand is written ok, but since I can only 
chose already 'taken' 3-letter-codes the refinement always crashes as there is 
a clash with existing library entries.
Is there any way around this? How do I add a novel ligand?

Thanks so much for your help.

Best wishes,
Stefanie




Dr. Stefanie Freitag-Pohl (she/her)

Durham University

Department of Chemistry

South Road, Durham

DH1 3LE

United Kingdom

0191 334 2596

stefanie.freitag-p...@durham.ac.uk



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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

[Andy Purkiss]

Dear Fred,

You need to register for the Windows (and other OS) installers if you want the 
stand-alone version of Shelx.

The form is at https://shelx.uni-goettingen.de/register.php

We have it running on Windows, although this version came with our Bruker X-ray 
generator.

Hope this helps,

Andy



From: CCP4 bulletin board  on behalf of Fred Vellieux 

Sent: 12 March 2024 09:38
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small 
molecule crystallography


External Sender: Use caution.


Hello and thanks for the reply.

My input file came from my checking SHELX manuals and SHELX instructions on the 
web, and trying to modify them to suit my case.

I tried olex2 on a Windows computer (somehow olex2 did not run on my Linux box, 
and only v1.3 was able to install on that Windows machine and not the latest 
v1.5). However, olex2 (the installation program) does not come with Shelx 
program executables, and I could not locate the installers for the shelx 
software on Windows.

Hence I am running SHELXL in line command mode on my Linux box.

Thank you again,

Fred.

On 12/03/2024 10:12, David Waterman wrote:
Hi Fred,

I find Olex2 and shelxle are both convenient interfaces to SHELXL refinement, 
that take care of some of the details of .ins file format for you. However, 
maybe you are stuck in the starting gate, depending on what is malformed in 
your input file. Where did your input files come from?

Cheers
-- David


On Tue, 12 Mar 2024 at 09:01, Fred Vellieux 
mailto:frederic.velli...@lf1.cuni.cz>> wrote:
Hi folks,

I have a simple question: is there an electronic bulletin board for
small-molecule crystallography? I have checked the list of CCP projects
and there is no CCP-project for small molecule crystallography in the list.

I am trying to run SHELXL, and it fails with the cryptic message "** BAD
ATOM OR UNKNOWN INSTRUCTION **".

The alternative for me would be of course to use software meant for
macromolecular cystallography (that I know) on small molecule
diffraction data. And using the small molecule coordinate files
transformed to a suitable format. I don't know if this is feasible or
even advised. Probably not.

Thanks,

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK

[Andy Purkiss-Trew]

Hi Ian and list,

I don't know about rejected postings, as I've not made any recently, but
I am getting two copies of each posting made and the second has gone
through the same server as below:

Received: from ms1.kissei.co.jp ([210.238.65.82]) by
a12536.general.kissei.co.jp (Lotus Domino Release 6.5.4FP2) with
ESMTP id 2007081510253541-2677 ; Wed, 15 Aug 2007 10:25:35 +0900
Received: from ictmailer1.itd.rl.ac.uk (ictmailer1.itd.rl.ac.uk
[130.246.192.56]) by ms1.kissei.co.jp (8.11.6/3.7W) with ESMTP
id l7F1PYJ20264 for [EMAIL PROTECTED]; Wed, 15 Aug 2007
10:25:34 +0900

Looks like problem with someone's e-mail system to me.

Andy

On Wed, 2007-08-15 at 11:03 +0100, Ian Tickle wrote:
 All - is anyone else getting this response every time they post a
 message or is it just me?  The received header shows
 [EMAIL PROTECTED] (ms1.kissei.co.jp [210.238.65.82]).
 
 -- Ian
 
  -Original Message-
  From: JISCMAIL LISTSERV Server (14.5) 
  [mailto:[EMAIL PROTECTED] 
  Sent: 15 August 2007 10:51
  To: Ian Tickle
  Subject: Rejected posting to CCP4BB@JISCMAIL.AC.UK
  
  Your message is  being returned to you unprocessed because  
  it appears to have
  already been distributed to the CCP4BB list. That is, a 
  message with identical
  text (but  possibly with different mail  headers) has been 
  posted  to the list
  recently, either by you or by someone  else. If you have 
  reason to resend this
  message to the list (for instance because you have been 
  notified of a hardware
  failure with loss of  data), please alter the text of the  
  message in some way
  and resend it  to the list. Note  that altering the 
  Subject:  line or adding
  blank lines at the top or bottom  of the message is not 
  sufficient; you should
  instead add a sentence or two at  the top explaining why you 
  are resending the
  message, so  that the other  subscribers understand  why they 
  are  getting two
  copies of the same message.
  
 
 
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+--+
| Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London |
|   E-mail   [EMAIL PROTECTED]|
+--+

Re: [ccp4bb] The CCP4 license is ambiguous

[Andy Purkiss]

Quoting Kjeldgaard Morten [EMAIL PROTECTED]:

  The CCP4 license does explicitly allow you to redistribute library  
  code
  Phil
 
 That's not the way I read the license. There are two sections of the  
 license that are contradictory, 2.1 and 2.2. Both place restrictions  
 on your use of the software. According to 2.1 you can distribute CCP4  
 software to third parties, but according to 2.2 you can't. 2.3 limits  
 the license to academic use. None of this is compliant with the GPL,  
 and the inclusion of GPL as appendixes to the CCP4 license is  
 incomprehensible at best, but could be viewed as fraudulent.
 

If you read the licence properly, you will see that section 2.1 covers the
libraries, whilst 2.2 covers the applications. 

It also reads to me, that the only software covered by the LGPL is any which
would come under section 2.5 and so is not covered by the CCP4 licence (much as
section 2.6 covers third party software included with its own licence, e.g.
Astexviewer). I don't have time to examine the licences for each bit of code,
but with software from so many sources, I'm sure that some of the code is under
the LGPL, and not the CCP4 licence.

-- 
We are the Kitten. Lower your weapons and open your arms. 
Your refrigerators and sofas will be utilized for our comfort. 
Your society will be assimilated to nurture and care for our own. 
Resistance is Furry.
+-+
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|   E-mail   [EMAIL PROTECTED]   |
+-+



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Re: [ccp4bb] Phaser TFZ=100.0 ?

[Andy Purkiss]

Quoting Andrew Wong [EMAIL PROTECTED]:

 I was using Phaser for some MR with a data set in P1 (may not actually be 
 P1, but..), and in every run I always got a list of solutions that all 
 have TFZ=100.0, with a very small LLG (around 0 or even in the negative). 
 The RFZ is like 4 or less. The solution(s) are definitely wrong, but I'm 
 just curious why Phaser is doing that? Could the TFZ=100.0 'solutions 
 possibly mask out the real solutions?
 

Is this not because the translation search has no fixed origin (for the first
molecule). In other words, all points are the same and placing the molecule
fixes the origin allowing search for a second molecule. I will check what my P1
search showed, when I get into work!


-- 
We are the Kitten. Lower your weapons and open your arms. 
Your refrigerators and sofas will be utilized for our comfort. 
Your society will be assimilated to nurture and care for our own. 
Resistance is Furry.
+-+
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|   E-mail   [EMAIL PROTECTED]   |
+-+



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